Academic literature on the topic 'Digitised specimens'

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Journal articles on the topic "Digitised specimens"

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Phillips, Carina. "Digitised Diseases." Bulletin of the Royal College of Surgeons of England 95, no. 5 (May 1, 2013): 164–65. http://dx.doi.org/10.1308/003588413x13643054409342.

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Over the past year RCS museum staff have been working on a project called Digitised Diseases. This Joint Information Systems Committee (JISC)-funded project is a collaboration with the university of Bradford and Museum of London Archaeology (MOLA). Digitised Diseases aims to bridge the gap between modern clinical medicine, historic medical collections and archaeological assemblages in the study of osteological pathology. The project will produce an archive of 3D case studies of exemplar specimens that can be studied virtually.
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Takano, Atsuko, Yasuhiko Horiuchi, Yu Fujimoto, Kouta Aoki, Hiromune Mitsuhashi, and Akira Takahashi. "Simple but long-lasting: A specimen imaging method applicable for small- and medium-sized herbaria." PhytoKeys 118 (February 18, 2019): 1–14. http://dx.doi.org/10.3897/phytokeys.118.29434.

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Major international herbaria, natural history museums and universities have recently begun to digitise their collections to facilitate studies and improve access to collections. In Japan, more than 10 million herbarium specimens are housed in various universities/museums; however, only 1% of these have been digitised. In this paper, we describe a new method for imaging herbarium specimens that is applicable to local/small herbaria. It is safe, fast, simple and inexpensive, but also satisfies usage guidelines for minimum image quality and can produce digital files suitable for long-term storage and future post production. During an eight-month trial at the Museum of Nature and Human Activities, Hyogo, with three part-time workers using a custom-made copy stand and a mirrorless interchangeable lens camera with a large LED light bank system, we were able to image 73,180 herbarium specimens (571 per day on average), obtaining two RAW and two JPEG files for each specimen.
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Astono, Indriani P., James S. Welsh, Christopher W. Rowe, and Phillip Jobling. "Objective quantification of nerves in immunohistochemistry specimens of thyroid cancer utilising deep learning." PLOS Computational Biology 18, no. 2 (February 28, 2022): e1009912. http://dx.doi.org/10.1371/journal.pcbi.1009912.

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Accurate quantification of nerves in cancer specimens is important to understand cancer behaviour. Typically, nerves are manually detected and counted in digitised images of thin tissue sections from excised tumours using immunohistochemistry. However the images are of a large size with nerves having substantial variation in morphology that renders accurate and objective quantification difficult using existing manual and automated counting techniques. Manual counting is precise, but time-consuming, susceptible to inconsistency and has a high rate of false negatives. Existing automated techniques using digitised tissue sections and colour filters are sensitive, however, have a high rate of false positives. In this paper we develop a new automated nerve detection approach, based on a deep learning model with an augmented classification structure. This approach involves pre-processing to extract the image patches for the deep learning model, followed by pixel-level nerve detection utilising the proposed deep learning model. Outcomes assessed were a) sensitivity of the model in detecting manually identified nerves (expert annotations), and b) the precision of additional model-detected nerves. The proposed deep learning model based approach results in a sensitivity of 89% and a precision of 75%. The code and pre-trained model are publicly available at https://github.com/IA92/Automated_Nerves_Quantification.
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Favret, Colin, Étienne Normandin, and Louise Cloutier. "The Ouellet-Robert Entomological Collection: new electronic resources and perspectives." Canadian Entomologist 151, no. 04 (June 20, 2019): 423–31. http://dx.doi.org/10.4039/tce.2019.34.

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AbstractThe Ouellet-Robert Entomological Collection (Université de Montréal, Montréal, Québec, Canada) is one of the largest and most important university collections in Canada. Although officially dedicated in 1984, much of the material in the collection dates to the 1930s and 1940s work of the Clerics of Saint Viator, Joseph Ouellet and Adrien Robert. In order to establish curatorial priorities, a collection profile was conducted grading eight criteria on a scale of 1–4, the most important being the conservation status of the specimens. A taxonomic inventory of the collection was also conducted, including the number of pinned specimens and alcohol vials, as well as a brief geographic description: whether or not at least one specimen of each species was collected in Québec or in North America. Finally, the specimen metadata for Odonata, Ephemeroptera, and Trichoptera were digitised. The inventory and specimen data can be downloaded at Canadensys.net. The collection houses approximately 1.5 million specimens, of which one-third are pinned, representing 20 000 species. Half of those species are recorded from Québec. The inventory and profile will be updated and the specimen database grown as portions of the collection are re-curated by personnel and volunteers, including the student-run organisation, “Club QMOR”.
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Aleksandrowicz, Oleg, Zbigniew Sobisz, Mariola Truchan, and Konrad Wiśniewski. "Przyrodnicze kolekcje naukowe Akademii Pomorskiej w Słupsku." Kosmos 70, no. 2 (September 12, 2021): 167–72. http://dx.doi.org/10.36921/kos.2021_2790.

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Pomeranian University in Słupsk hosts two significant natural history collections, i.e. the Herbarium Slupensis (SLTC) botanical collection and the zoological collection, which contains mainly the arthropods. In the Herbarium both the historical and contemporary material is stored, including fungi, lichens, bryophytes and vascular plants that were collected mainly in the Polish Pomerania. The zoological collection contains predominantly the specimens of beetles and spiders, originating from Belarus and Poland (from Pomerania, but also from Masuria and Lower Silesia). In the two collections there are representatives of very valuable species. Both the Herbarium and the zoological collection are presently being digitised, supplemented with new specimens and developed. They present a significant contribution to knowledge on diversity of fauna and flora in the region and in Poland.
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Rokrok, B., K. Edalati, E. Yahaghi, N. Mohammadzadeh, N. Rastkhah, and A. Movafeghi. "Three-dimensional mapping of non-complex specimens by image processing and optical density evaluation of digitised radiographs." Insight - Non-Destructive Testing and Condition Monitoring 51, no. 6 (June 2009): 315–20. http://dx.doi.org/10.1784/insi.2009.51.6.315.

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Khidas, Kamal, and Stéphanie Tessier. "Building Next-Generation Collections: Natural History Specimens, Just One Click Away!" Biodiversity Information Science and Standards 2 (July 4, 2018): e26145. http://dx.doi.org/10.3897/biss.2.26145.

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Digitisation has made significant advances in many natural history collections since the 1980s. The Vertebrate Zoology Collections team of the Canadian Museum of Nature (CMNVZC; ca. 1,250,000 catalogued specimens) has the ambition to go fully digital with our physical objects and associated data. Organising CMNVZC data electronically (primary digitisation) through computerisation for collection management purposes was initiated in 1972 and systematically implemented since the 1980s. This databasing process involved several stages, each with its own objectives and challenges. It resulted in ca. 100% of the CMNVZC being now digitised and core specimen data being retrievable from the Web (e.g., GBIF, and VertNet). Digitising requires regular updates to reflect the changing needs of the collections-based research community, and to capitalise on new opportunities that arise with the advances in technology. In this digital age, improving collections accessibility and usability through realistic and sustainable digitisation, while avoiding the downside of information overload, remains the most pressing challenge. Increasing CMNVZC accessibility necessitates further consolidation and information standardisation of various types (e.g. collecting data) to be retrieved from several sources (e.g., field notes, original data sheets, and maps). Optimising collections usability can be achieved by adding value to existing records (secondary digitisation) by means of additional information as mentioned above, georeferencing, as well as 2D and 3D imaging. Virtual sharing of 3D specimen images allows for remote examination of specimens usually inaccessible through loans, such as type and rare specimens, and the possibility for morphometric analyses. Digital imaging of the vertebrate collection, however, represents a major challenge given the complexity and variation of shapes and sizes among specimens. Limitations of current 3D surface imaging technology, none of which have been specifically designed for natural history specimens, hamper CMNVZC imaging workflows. Digital tools are key to the success of increasing usability of natural history collections and play an important role in preserving information. Digitisation activities should endeavour to improve online access of physical objects and their full array of data with optimized usability.
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Kanavati, Fahdi, Naoki Hirose, Takahiro Ishii, Ayaka Fukuda, Shin Ichihara, and Masayuki Tsuneki. "A Deep Learning Model for Cervical Cancer Screening on Liquid-Based Cytology Specimens in Whole Slide Images." Cancers 14, no. 5 (February 24, 2022): 1159. http://dx.doi.org/10.3390/cancers14051159.

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Liquid-based cytology (LBC) for cervical cancer screening is now more common than the conventional smears, which when digitised from glass slides into whole-slide images (WSIs), opens up the possibility of artificial intelligence (AI)-based automated image analysis. Since conventional screening processes by cytoscreeners and cytopathologists using microscopes is limited in terms of human resources, it is important to develop new computational techniques that can automatically and rapidly diagnose a large amount of specimens without delay, which would be of great benefit for clinical laboratories and hospitals. The goal of this study was to investigate the use of a deep learning model for the classification of WSIs of LBC specimens into neoplastic and non-neoplastic. To do so, we used a dataset of 1605 cervical WSIs. We evaluated the model on three test sets with a combined total of 1468 WSIs, achieving ROC AUCs for WSI diagnosis in the range of 0.89–0.96, demonstrating the promising potential use of such models for aiding screening processes.
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Zeko, Antonija, Vedran Šegota, Tihana Vilović, Nikola Koletić, and Antun Alegro. "Aquatic plants of Croatia: Data derived from the ZA herbarium collection." Natura Croatica 29, no. 2 (March 31, 2021): 205–16. http://dx.doi.org/10.20302/nc.2020.29.27.

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As many as 963 herbarium sheets featuring 76 aquatic plant taxa from the ZA collection were digitised and published online through the Virtual Herbarium. Aquatic plants have been collected over a period of 176 years, with three peaks (second decade of the 20th century, in the 1940s and 1950s, and in the current decade). Most of the specimens were collected in Croatia and a smaller number in neighbouring and geographically close countries. The importance of the collection is expressed through the specimens of many rare and threatened species, because it represents the only evidence of their presence in Croatia (the regionally extinct Caldessia parnassifolia, as well as Luronium natans, Callitriche platycarpa, C. truncata, C. hermaphroditica, Potamogeton alpinus, P. compressus, P. polygonifolius, Nuphar × spenneriana and Sparganium minimum). The collection in ZA is a valuable source of data about the historical and recent distribution of aquatic plants that constitute a foundation for the estimation of distribution changes, threat assessment and conservation policies.
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Dwivedi, A. K. "Morphometric variations between seasonal migrants of anadromous shad Tenualosa ilisha (Hamilton, 1822) from Hooghly Estuary, India." Marine and Freshwater Research 70, no. 10 (2019): 1427. http://dx.doi.org/10.1071/mf19004.

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The morphometric variations between two seasonal migrants (winter and monsoon) of anadromous shad Tenualosa ilisha from Hooghly Estuary were evaluated and compared using geometric morphometrics (GM). Altogether, 128 fish samples of T. ilisha, comprising 64 samples each from winter and the monsoon season, were collected for two successive years (2017 and 2018) and 14 landmarks were digitised uniformly on each individual. Relative warps (RW), principal component analysis (PCA), canonical variate analysis (CVA) and discriminant function analysis (DFA) were used to determine shape variations between seasonal runs. The deformation grid of RW showed that monsoon specimens have a deeper body profile, whereas winter specimens have a slender body profile. The PCA showed low variance (40.45% for first two principal components) and high overlap among all the groups. The CVA-extracted Mahalanobis and Procrustes distances (3.473 and 0.032 respectively) between the two groups (winter and monsoon) were highly significant (P<0.0001). The DFA also separated two groups with high cross-validated classification rates (85.94 and 95.31% of winter and monsoon specimens respectively were correctly classified). Hence, the results of RW, CVA and DFA clearly indicate the existence of two morphologically distinct units of T. ilisha in Hooghly Estuary.
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Dissertations / Theses on the topic "Digitised specimens"

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Wilson, Andrew S., Keith Manchester, Jo Buckberry, Rebecca A. Storm, and Karina T. Croucher. "Digitised Diseases: Seeing Beyond the Specimen to Understand Disease and Disability in the Past." 2016. http://hdl.handle.net/10454/10226.

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Digitised Diseases is a major web-based 3D resource of chronic disease conditions that manifest change to the human skeleton. The resource was established through funds from Jisc, the University of Bradford and Bradford Visualisation. The multidisciplinary team involving project partners Museum of London Archaeology and the Royal College of Surgeons of England undertook a program of mass digitization of pathological type specimens from world-renowned archaeological, historic and medical collections at the University of Bradford, in London and York. We continue to augment this resource through ingestion of new content. The resource was always envisaged as needing to appeal to a diverse user community, having impact not just among academic and clinical beneficiaries, but also enriching the wider understanding of public health in the past. From the outset, our focus was on making sure that the digitized paleopathological exemplars were represented and understood within a broader clinical context. In essence we wanted to emphasize the impact of living with disease and disability in an era before modern therapies were available and the significance of care provision that would have been required at a societal level, given the longevity of many of these conditions.
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Book chapters on the topic "Digitised specimens"

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Osis, Francis. "“Inform the Head, Give Dexterity to the Hand, Familiarise the Heart”: Seeing and Using Digitised Eighteenth-Century Specimens in a Modern Medical Curriculum." In Advances in Experimental Medicine and Biology, 163–79. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-61125-5_9.

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Wilson, Andrew S., Keith Manchester, Jo Buckberry, Rebecca Storm, and Karina Croucher. "Digitised Diseases: Seeing Beyond the Specimen to Understand Disease and Disability in the Past." In New Developments in the Bioarchaeology of Care, 301–15. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-39901-0_16.

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Akbar, Zaenal, Wita Wardani, Taufik Mahendra, Yulia A. Kartika, Ariani Indrawati, Tutie Djarwaningsih, Lindung P. Manik, and Aris Yaman. "Semantic Annotation of Objects of Interest in Digitized Herbarium Specimens for Fine-Grained Object Classification." In Semantic Web Technologies, 181–202. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003309420-8.

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Triki, Abdelaziz, Bassem Bouaziz, Jitendra Gaikwad, and Walid Mahdi. "PhenoDeep: A Deep Learning-Based Approach for Detecting Reproductive Organs from Digitized Herbarium Specimen Images." In Neural Information Processing, 402–13. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-92185-9_33.

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Abbott, John C., and Emily L. Sandall. "Odonata collections and databases." In Dragonflies and Damselflies, 327–40. 2nd ed. Oxford University PressOxford, 2022. http://dx.doi.org/10.1093/oso/9780192898623.003.0023.

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Abstract The Odonata community has embraced the benefits afforded by the digital age to access specimens, promote and disseminate data, engage with an ever-growing community of enthusiasts, and answer big questions. Global databases offer the capacity to move beyond simple catalogs, link data and data providers, and create a unified and engaged community. There are millions of odonate specimens currently housed in institutional and private collections, with relatively few digitized and/or imaged. This chapter addresses approaches to data capture, including best practices when digitizing museum collections, ways to enhance the value of specimen data, integration of the Big Data of genetic and phenotypic databases, workflows for efficiency of data capture, and how the large and growing odonate enthusiast community can contribute to these efforts. It also covers how some of these digital efforts are resulting in fewer physical specimens being collected in recent years.
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Conference papers on the topic "Digitised specimens"

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Butts, Susan H., Talia S. Karim, and Christopher A. Norris. "IDIGPALEO: EDUCATION AND OUTREACH USING DIGITIZED MUSEUM SPECIMENS." In GSA Annual Meeting in Seattle, Washington, USA - 2017. Geological Society of America, 2017. http://dx.doi.org/10.1130/abs/2017am-305591.

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"Virtual Pathology Learning Resource is proving to be an effective strategy in teaching Pathology to allied health science students." In InSITE 2018: Informing Science + IT Education Conferences: La Verne California. Informing Science Institute, 2018. http://dx.doi.org/10.28945/3972.

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Aim/Purpose: [This Proceedings paper was revised and published in the 2018 issue of the journal Issues in Informing Science and Information Technology, Volume 15] The aim of this study was to concept test a novel instructional aid called Virtual Pathology Learning Resource (VPLR), which was used as a vehicle to communicate information, and enhance teaching and learning of basic sciences (Anatomy, Physiology and Pathology) to allied health science students at a South Australian university. Background: Pathology was traditionally taught using potted specimens to independently review macroscopic features of disease. However, this approach alone was found inadequate and ineffective. For one, the potted specimens were not easily accessible for all students. VPLR is a new teaching platform comprising of digitised human normal and human pathology specimens (histology, histopathology), patient case studies, short answer and critical thinking questions, and self-assessment quizzes. Using authentic learning theory as an educational approach, this learning resource was developed to enhance the teaching and learning of Pathology. Methodology: A cross-sectional study design was used. A survey, administered at the conclusion of the course, gathered qualitative and quantitative data concerning the perceptions and experiences of the students about VPLR. The online tool SurveyMonkey was utilised so that students could respond anonymously to a web link that displayed the questionnaire. The effectiveness of the program and its perceived impact on students was assessed using a 18-item questionnaire seeking agreement or disagreement with statements about VPLR, and open-ended questions querying the best things about VPLR, benefits to be derived, and areas for improvement. Descriptive and frequency analyses were performed. Contribution: The VPLR approach involved rich learning situations, contextualised content, and facilitated greater understanding of disease concepts and problems. Findings: In a sample of 103 Medical Radiation students, 42% of students (N=43) responded to the post-intervention survey. The majority of students reported highly positive effects for each component of the VPLR. The overall results indicated that this tool was an effective strategy in teaching Pathology as it assisted students' gaining knowledge and developing professional imaging skills. Recommendations for Practitioners: As students found VLPR to be beneficial, it is recommended that the same approach be applied for teaching of Pathology to other allied health students, such as Nursing. Other universities might consider adopting this innovation for their courses. Recommendation for Researchers: Applying VPLR to other allied health science students will be undertaken next. This innovation will be appropriate for other health science students with particular emphasis on case-based or problem-based learning, and combined with clinical experiences. Impact on Society: In reshaping the way of teaching a science course, students are benefited by a greater depth of understanding of content, and increase motivation with study. These are important to keep students engaged and prepared for practice. VPLR may impact on education and technology trends so that continuous exploration and possibilities of initiatives are ongoing to help students be successful learners. Other impacts are the new forms of learning discovered, and the renewed focus on group work and collaboration and the use of technology in innovation. Future Research: Future directions of this research would be to conduct a follow-up of this cohort of students to determine if the impacts of the innovation were durable, that means the change in perceptions and behaviour are sustained over time.
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Hammouda, K., F. Khalifa, M. Ghazal, H. E. Darwish, J. Yousaf, and A. El-Baz. "A Pyramidal CNN-Based Gleason Grading System Using Digitized Prostate Biopsy Specimens." In 2022 26th International Conference on Pattern Recognition (ICPR). IEEE, 2022. http://dx.doi.org/10.1109/icpr56361.2022.9956244.

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Triki, Abdelaziz, Bassem Bouaziz, Walid Mahdi, and Jitendra Gaikwad. "Objects Detection from Digitized Herbarium Specimen based on Improved YOLO V3." In 15th International Conference on Computer Vision Theory and Applications. SCITEPRESS - Science and Technology Publications, 2020. http://dx.doi.org/10.5220/0009170005230529.

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Schrade, Marcus, Stephan Staudacher, and Matthias Voigt. "Experimental and Numerical Investigation of Erosive Change of Shape for High-Pressure Compressors." In ASME Turbo Expo 2015: Turbine Technical Conference and Exposition. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/gt2015-42061.

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Compressor performance and maintenance characteristics of jet engines are highly influenced by erosion caused by ingested, solid particles. For a meaningful prediction of these characteristics, an adequate modeling of the erosive change of shape of compressor blades is necessary. This article investigates the erosive change of shape of two different specimens (cylinder and compressor blade) out of aluminum alloy EN AW-6060 both experimentally and numerically. The erosion experiments were performed with a test rig using different amounts of standardized Arizona Test Dust A3 (particle sizes of 1–120μm) to acquire the time-dependent change of shape of the specimens. The shape of the specimens was digitized using a strip projection technique before and after each erosion test. The test rig provides boundary conditions specific for first stages of axial high-pressure compressors of jet engines in terms of relative fluid velocity (350ms−1) which is the main parameter of erosion. Numerical results were obtained with a model predicting the time-dependent change of shape of the specimens in 2D. The numerical model uses erosion rate curves that were experimentally determined in the same test rig using flat plates out of the aforementioned aluminum alloy. Thus, we were able to investigate experimentally the time-dependent erosive change of shape of the specimens and compare it with the numerical predictions. We conclude that the numerical model is a valid approach to predict erosive change of shape for different specimen geometries and materials, when erosion rate curves are available for these materials.
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Karim, Talia. "Insights from the Thematic Collections Networks and beyond on using digitized specimens for education and outreach." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.104565.

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Litjens, G., B. Ehteshami Bejnordi, N. Timofeeva, G. Swadi, I. Kovacs, C. Hulsbergen-van de Kaa, and J. van der Laak. "Automated detection of prostate cancer in digitized whole-slide images of H and E-stained biopsy specimens." In SPIE Medical Imaging, edited by Metin N. Gurcan and Anant Madabhushi. SPIE, 2015. http://dx.doi.org/10.1117/12.2081366.

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Moran, Sean M., Richard C. Hulbert, Warren H. Brown, and Bruce J. MacFadden. "INCREASING THE RESEARCH POTENTIAL OF DIGITIZED FOSSILS: A PILOT STUDY USING SPECIFY TO ATTACH STABLE ISOTOPE DATA TO VOUCHERED MUSEUM SPECIMENS." In GSA Annual Meeting in Denver, Colorado, USA - 2016. Geological Society of America, 2016. http://dx.doi.org/10.1130/abs/2016am-280994.

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Okada, Mitsutoshi, Toshihiko Takahashi, Susumu Yamada, Takayuki Ozeki, and Tomoharu Fujii. "Development of Temperature Estimation Method for a Gas Turbine Transition Piece." In ASME Turbo Expo 2016: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/gt2016-56182.

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Temperature estimation methods for a transition piece of a gas turbine are developed in terms of microstructural changes and computational fluid dynamics (CFD) for life assessment. Temperature is estimated to be low around the center of the component where thermal barrier coating (TBC) is deposited on the Ni-base superalloy and a combination of internal cooling and film cooling is also applied. Test specimens are prepared from the above area for a high-temperature heating test in air. The microstructure in the superalloy and TBC is investigated after the test. The thermally grown oxide (TGO) formed on the bondcoat surface increases with the square root of the test time, and on the basis of this relation, a temperature-estimation equation is obtained. The estimated temperature distribution is compared with a numerical heat transfer simulation by means of CFD. The geometry of the transition piece with internal cooling structure is acquired using an X-ray computerized radiography and a laser digitizer, and it is modeled for the numerical simulation. The heat conduction analysis is applied to the transition piece, and the convection and radiation heat transfer analyses are applied to the gas path and internal cooling flow. These analyses are conjugated to estimate the temperature distribution. The simulation result agrees well with the estimation using TGO thickness.
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